Butternut Squash Stuffed Shells

GFGluten FreeOFOil FreeVVegan
5 from 2 votes
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These Butternut Squash Stuffed Shells are baked in a rich and creamy vegetable sauce and stuffed with a healthy homemade vegan ricotta filling. Indulge in this classic comfort food made with a seasonal twist! Vegan, Gluten-Free & Oil-Free Option.

Table of Contents
  1. What You Need for Butternut Squash Stuffed Shells
  2. How to Make Butternut Squash Stuffed Shells
  3. Serving Suggestions
  4. How to Store Stuffed Shells
  5. Substitutions and Variations
  6. Recipe FAQs: 
  7. Butternut Squash Stuffed Shells Recipe

Behold – the vegan stuffed shells recipe you didn’t know you needed. This Butternut Squash Stuffed Shells recipe is made with ricotta filled jumbo pasta shells smothered in an ultra-smooth butternut squash cream sauce. Everything you want in a fall vegan pasta and more. I promise the extra effort is worth the end result! 

butternut squash stuffed shells with serving spoon

A Fall Twist on Cheesy Pasta Shells

This recipe is very similar to my original Vegan Stuffed Shells, but incorporates some of my favorite fall flavors – sweet butternut squash, warm cinnamon, fresh rosemary, and roasted garlicky goodness.  

If you ask me, butternut squash’s greatness is overshadowed by the popularity of pumpkin this time of year! Don’t get me wrong, pumpkin is great too, but butternut squash is slightly more flavorful and is also a better source of vitamin A, vitamin C, iron and fiber. 

Check out some of my other favorite butternut squash recipes: Fall Farro Salad, Butternut Squash & Brown Rice Casserole, Roasted Butternut Squash Hummus, or Butternut Squash and Apple Soup

What You Need for Butternut Squash Stuffed Shells

ingredients for butternut squash stuffed shells on kitchen countertop

This recipe is made with three components: 

  • Creamy Butternut Squash Sauce: Instead of using the classic marinara sauce, we’re baking these stuffed shells in a delicious butternut squash sauce made with ingredients like roasted garlic, cashews, oat milk, and cinnamon for a hint of warmth. 
  • Vegan Ricotta Mixture: I’ve been using my own vegan ricotta to make cheesy recipes like Zucchini Lasagna Roll Ups and Tomato Galettes and I’ve yet to be disappointed. If you’re short on time, opt for your favorite store-bought vegan ricotta. 
  • Pasta Shells: Any jumbo-sized pasta shells should do here. Most store-bought pasta is made without eggs and is naturally vegan-friendly.

How to Make Butternut Squash Stuffed Shells

collage of step by step photos for making butternut squash stuffed shells
  1. Toss the vegetables with a drizzle of oil and roast for 30 minutes, flipping the squash and shallots halfway through.
  2. Par-Cook your pasta shells. Drain and rinse with cold water, then spread the shells across a baking sheet to prevent sticking.
  3. Process the vegan ricotta ingredients together until a smooth cheese forms.
  4. Blend the shallots, roasted garlic, and ⅓ of the butternut squash together with remaining sauce ingredients until smooth. Season with additional salt and pepper as desired.
  5. Combine the stuffed shell filling ingredients until incorporated. 
  6. Pour 2 cups of sauce in the bottom of the baking dish.
  7. Stuff the shells with 1 tablespoon of the filling, then pour the remaining sauce over top along with a sprinkle of vegan cheese.
  8. Bake on the top rack of the oven for 20-25 minutes or until bubbly. 

Caitlin’s Cooking Tips

  • Chop the squash finely. This will allow it to cook faster and be easier to stuff into the pasta shells.
  • Squeeze the moisture out of the spinach. After you thaw the frozen spinach, squeeze as much excess water out of the spinach as possible. This will prevent your filling from being watery. 
butternut squash shells topped with vegan cheese in baking dish

Serving Suggestions

Serve these fall-inspired stuffed shells with one of my favorite kale salads: Kale Apple Walnut Salad, Winter Kale Salad or Kale and Cranberry Salad. It would also be delicious with a simple side of Easy Garlic Green Beans or Balsamic Marinated Mushrooms.

If you’re looking for more cheesy pasta bakes, you’ll also love this Vegan Pumpkin Mac & Cheese, Vegan Jalapeno Popper Pasta Bake and this Vegan Chorizo Pasta! You’ll also love my quick and easy dump & bake recipes!

How to Store Stuffed Shells

Leftover stuffed shells are best stored in the fridge in an airtight container and eaten within 5 days. To reheat multiple servings, heat the oven to 375F and cook leftovers tightly covered with tinfoil for 20 to 25 minutes, or until warmed through. Alternatively, place an individual serving in a microwave-safe bowl and reheat on high powder in 30 second intervals until warmed through. 

I have not attempted to freeze this stuffed shell recipe, but if you have success, please let me know! 

fork cutting through stuffed shell on white plate

Substitutions and Variations

  • Gluten-free option: Swap the wheat jumbo pasta shells for gluten-free pasta shells. The remainder of the recipe is naturally gluten-free. Corn and rice versions will hold up best without breaking.
  • Oil-free option: This recipe is naturally oil-free aside from the 1 tablespoon olive oil in the sauce and additional sprinkle of cheese. To make oil-free, omit the oil and dairy-free mozzarella and dry roast the vegetables. 
  • Use store-bought vegan ricotta: If you are short on time, use a store-bought vegan ricotta from brands like Kite Hill or Tofutti. 
  • Make ahead option: The roasted vegetables, vegan ricotta, and cream sauce can all be prepared up to 3 days in advance. Then, once ready, cook the pasta and fill the stuffed shells. 
  • Oat milk substitution: Soy milk is a great alternative that is similarly rich and creamy. 
vegan butternut squash stuffed shells in baking dish before covering with sauce

Recipe FAQs: 

Is manicotti the same as stuffed shells?

Manicotti and jumbo shells are similar in that they are both pastas typically stuffed with cheese, but they are different shapes. Manicotti are large hollow tubes and jumbo stuffed shells are large conchiglie pasta. 

How long do I boil jumbo shells?

If your pasta box does not include cooking times for making stuffed shells, cut the full cook time in half, then add two minutes. This will cook the pasta al dente, and prevent it from overcooking during the bake time. 

What is the best way to cut butternut squash?

Cutting a whole butternut squash can be intimidating, but it is a lot easier than it looks! Start by cutting off both ends, then cutting the butternut in half crosswise. Remove the skin with either a vegetable peeler or a sharp knife. Once peeled, cut the butternut in half lengthwise and scoop out the seeds. Then, finely cube and roast! For an easy visual, check out this quick video tutorial!

Which brands of vegan cheese or parmesan do you recommend?

Violife is one of my favorite go-to brands, but Follow Your Heart is also great!

Enjoy! If you make this recipe and decide to share it on Facebook or Instagram, don’t forget to tag me @FromMyBowl + #FromMyBowl! I would also love it if you could leave a comment below with a recipe rating! Thank you for the support 😊 

butternut squash stuffed shells in baking dish with golden spoon

Butternut Squash Stuffed Shells

5 from 2 votes
Prep Time 30 minutes
Cook Time 50 minutes
Total Time 1 hour 20 minutes
Servings 8 people
These Butternut Squash Stuffed Shells are baked in a rich and creamy vegetable sauce and stuffed with a healthy homemade vegan ricotta filling. Indulge in this classic comfort food made with a seasonal twist! Vegan, Gluten-Free & Oil-Free Option.


For the Roasted Vegetables

  • 4 cups butternut squash peeled and diced (about 1 medium)
  • 2 shallots peeled and cut in half
  • 1 head garlic
  • 1/2 tsp kosher salt
  • black pepper to taste
  • olive oil for drizzling

For the Vegan Ricotta (or use store-bought)

For the Sauce

  • 2/3 cup roasted butternut squash above
  • roasted shallots and garlic above
  • 1/2 cup raw cashews soaked for at least 4 hours
  • 1 tbsp olive oil optional; for a smoother sauce
  • 1/4 tsp cinnamon optional
  • 1 1/2 cup vegetable broth
  • 1 cup full-fat oat or cashew milk
  • salt and black pepper to taste

For the Stuffed Shells

  • 1 pound jumbo pasta shells gluten-free if necessary
  • Vegan Ricotta above
  • 2 cup roasted butternut squash above
  • 6 ounces frozen spinach thawed and pressed well
  • 1 tbsp finely chopped rosemary
  • salt and black pepper to taste
  • 1 cup dairy-free mozzarella or parmesan optional


  • Prep: Preheat the oven to 425F. Set two baking sheets aside and bring a large pot of salted water to a boil for the pasta.
  • Roast the Vegetables: Cut the top 1/4” off of the head of garlic to expose most of the cloves. Place on a sheet of aluminum foil, then drizzle with oil and wrap it up to seal it tightly. Add the butternut squash and shallots to the baking sheet and drizzle with oil, salt, and pepper to taste. Use your hands to toss until evenly coated, then spread the vegetables out evenly on the baking sheet. Add the foil-wrapped garlic to the baking sheet as well. Bake for 30 minutes, flipping the squash and shallots halfway through cooking. 
  • Cook the Pasta:  In the meantime, add the pasta shells to the boiling pot of water and cook following the pre-boil or stuffed shell instructions, stirring occasionally. If the package does not have instructions, cut the cooking time of the pasta in half, then add two minutes. Drain and rinse with cold water, then spread the shells across a baking sheet in a single layer to prevent sticking.
  • Make the Ricotta:add the tofu, cashews, nutritional yeast, garlic, lemon juice, and salt to a food processor with the S-blade attached. Process for 45 to 60 seconds, scraping the sides as necessary, until a smooth texture forms. Set aside.
  • Blend the Sauce: add only ⅓ (roughly ½ cup; 75 g) of the roasted butternut squash to a blender along with the roasted shallots. Carefully remove the garlic bulb from the tin foil and squeeze the cloves into the blender as well. Add the cashews, oil (if using), cinnamon, black pepper, broth, and milk to the blender. Blend on high for 45 to 60 seconds, or until a smooth sauce forms. Taste the sauce and season with additional salt or pepper if necessary.
  • Make the filling: place the prepared ricotta in a large mixing bowl and add in the remaining roasted butternut squash, spinach, rosemary, salt, and black pepper to taste. Mix well with a spatula until everything is evenly incorporated.
  • Stuff the shells: Pour 2 cups of sauce in the bottom of the baking dish. Fill each cooked shell with ~1 tablespoon of filling, then place in the baking dish. Repeat with the remaining shells, then pour the remaining sauce on top. Sprinkle the cheese over the tops of the shells, if using. 
  • Bake: Bake in the top rack of the oven for 20-25 (?) minutes, until the sauce is bubbly and cheese has melted. 

Recipe Notes

  • Frozen Spinach: thaw the frozen spinach and squeeze as much liquid out of it as possible before adding to the ricotta mixture.
  • Gluten-Free: this recipe can be made gluten-free by using gf jumbo shells. 
  • Make Ahead: The roasted squash, ricotta, and cream sauce can all be made up to 3 days in advance. Just store in the fridge until you are ready to use!


Calories: 358kcalCarbohydrates: 42gProtein: 16gFat: 16gSaturated Fat: 3gPolyunsaturated Fat: 4gMonounsaturated Fat: 8gTrans Fat: 0.001gSodium: 477mgPotassium: 604mgFiber: 5gSugar: 7gVitamin A: 9997IUVitamin C: 21mgCalcium: 191mgIron: 4mg
Keyword: vegan stuffed shells, vegan stuffed shells, butternut squash recipes
Course: Main, Main Course
Method: Oven, Stovetop
Cuisine: American
Diet: Gluten Free, Vegan, Vegetarian

About the Author

Hey there, I’m Caitlin! I make easy-to-follow, wholesome, and budget-friendly vegan recipes that are mostly gluten-free and refined sugar-free. I’m also an avid yogi, love the great outdoors, am chocolate-obsessed, and enjoy eating almond butter straight off of the spoon.

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    1. Yes, but you would need to cook it down first and try to remove as much liquid as possible. You’d probably need to cook 12 – 16 ounces of fresh spinach down to get the same amount, volume-wise.

  1. 5 stars
    These were so tasty! I made them for my Christmas dinner to add to the spread (my family eats meat but I do not) and everyone loved them! So delicious. I made the tofu ricotta in advance which was helpful.

  2. Hi Caitlin, the sauce tastes absolutely amazing but unfortunately it came out super runny when I followed the recipe as written. I needed to add another cup of both squash and cashews to thicken it up. Next time I would definitely 1/2 the liquids or plan to double the solids!

      1. To be safe I went ahead thickened it with the extra squash and cashews prior to baking and it turned out great! But perhaps next time I will see how it does without the added solids.

      1. I doubled this recipe and made it with lasagna noodles (only because I could not find large shells at nearby grocery stores). You will need less lasagna noodles (by weight) than shells. The tofu ricotta and butternut squash was really good. I will remake this recipe with less plant milk as I prefer a thicker consistency. (The sauce dried out/thickened in the oven a bit but not enough for my liking as the dish had a very watered down flavor. This recipe is great as is, but I personally would add my plant milk last and in intervals until I reach my desired consistency.)

  3. I’m not seeing any instructions beyond “Blend the sauce” or “Make the filling”, subtitles without actual text instructions. That’s a tad too sparse to go by.

    1. Hi Ali, sorry to hear that. Is it visible now? There should be full instructions next to each of those subtitles.